Added link to overview chapter + tweaked README

.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 docs
 tests/testthat/Rplots.pdf
+inst/doc

DESCRIPTION

@@ -77,3 +77,4 @@ Suggests:
 Config/testthat/edition: 3
 Depends: 
     R (>= 2.10)
+VignetteBuilder: knitr

README.Rmd

@@ -16,17 +16,34 @@ knitr::opts_chunk$set(
 # moiraine <img src="man/figures/logo.png" align="right" alt="" width="120" />
 
 <!-- badges: start -->
-[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 <!-- badges: end -->
 
-`moiraine` is a package for facilitating the construction of a reproducible analysis pipeline for multi-omics data integration. It provides functions to automate data import, pre-processing, transformation, integration through several tools, as well as interpretation and comparison of the integration results. It relies on the [targets](https://books.ropensci.org/targets/) package to generate reproducible workflows. `moiraine` currently supports multi-omics data integration through:
+`moiraine` is a package for facilitating the construction of a reproducible analysis pipeline for multi-omics data integration. It provides functions to automate data import, pre-processing, transformation, integration through several tools, as well as interpretation and comparison of the integration results. It relies on the [targets](https://books.ropensci.org/targets/) package to generate reproducible workflows.
 
--   sPLS and DIABLO from the mixOmics package;
+## Overview
 
--   sO2PLS from the omicsPLS package;
+The workflow for a typical multi-omics integration analysis handled with `moiraine` includes the following steps:
 
--   MOFA and MEFISTO from the MOFA2 package.
+* Data import: this covers the import of omics measurements as well as associated metadata (i.e. information about the omics features and samples) -- moiraine relies on the [`MultiDataSet` package](https://bioconductor.org/packages/release/bioc/html/MultiDataSet.html) to store this information in a consistent format;
 
+* Inspection of the omics datasets: including checking values density distribution, samples overlap between omics datasets, or presence of missing values;
+
+* Preprocessing of the omics datasets: missing values imputation, transformation, and pre-filtering of samples and omics features;
+
+* Integration of the omics datasets by one or more of the supported tools; currently, the following integration methods are covered in `moiraine`:
+
+  * sPLS and DIABLO from the `mixOmics` package
+
+  * sO2PLS from the `OmicsPLS` package
+
+  * MOFA and MEFISTO from the `MOFA2` package
+
+* Interpretation of the integration results using standardised visualisations enriched with features and samples metadata;
+
+* Comparison of the integration results obtained by different methods or pre-processing approaches.
+
+An overview of the capabilities of the package is available [here](https://solid-lamp-kq546rq.pages.github.io/overview.html).
 
 ## Installation
 

README.md

@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-[![Project Status: WIP – Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
-public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 <!-- badges: end -->
 
 `moiraine` is a package for facilitating the construction of a
@@ -16,14 +16,44 @@ provides functions to automate data import, pre-processing,
 transformation, integration through several tools, as well as
 interpretation and comparison of the integration results. It relies on
 the [targets](https://books.ropensci.org/targets/) package to generate
-reproducible workflows. `moiraine` currently supports multi-omics data
-integration through:
+reproducible workflows.
 
-- sPLS and DIABLO from the mixOmics package;
+## Overview
 
-- sO2PLS from the omicsPLS package;
+The workflow for a typical multi-omics integration analysis handled with
+`moiraine` includes the following steps:
 
-- MOFA and MEFISTO from the MOFA2 package.
+- Data import: this covers the import of omics measurements as well as
+  associated metadata (i.e. information about the omics features and
+  samples) – moiraine relies on the [`MultiDataSet`
+  package](https://bioconductor.org/packages/release/bioc/html/MultiDataSet.html)
+  to store this information in a consistent format;
+
+- Inspection of the omics datasets: including checking values density
+  distribution, samples overlap between omics datasets, or presence of
+  missing values;
+
+- Preprocessing of the omics datasets: missing values imputation,
+  transformation, and pre-filtering of samples and omics features;
+
+- Integration of the omics datasets by one or more of the supported
+  tools; currently, the following integration methods are covered in
+  `moiraine`:
+
+  - sPLS and DIABLO from the `mixOmics` package
+
+  - sO2PLS from the `OmicsPLS` package
+
+  - MOFA and MEFISTO from the `MOFA2` package
+
+- Interpretation of the integration results using standardised
+  visualisations enriched with features and samples metadata;
+
+- Comparison of the integration results obtained by different methods or
+  pre-processing approaches.
+
+An overview of the capabilities of the package is available
+[here](https://solid-lamp-kq546rq.pages.github.io/overview.html).
 
 ## Installation
 

_pkgdown.yml

@@ -11,6 +11,8 @@ navbar:
   title: targets
   type: default
   left:
+  - text: Overview
+    href: https://solid-lamp-kq546rq.pages.github.io/overview.html
   - text: Reference
     href: reference/index.html
   - text: Manual